Chan Jacqueline, Holdstock Jolyon, Shovelton John, Reid James, Speight Graham, Molha Duarte, Pullabhatla Venu, Carpenter Stephanie, Uddin Ezam, Washio Takanori, Sato Hiroko, Izumi Yuuki, Watanabe Reiko, Niiro Hayato, Fukushima Yoshiyuki, Ashida Naoko, Hirose Takashi, Maeda Akiko
Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom.
Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan.
PLoS One. 2024 Jun 13;19(6):e0305422. doi: 10.1371/journal.pone.0305422. eCollection 2024.
Inherited retinal dystrophies comprise a clinically complex and heterogenous group of diseases characterized by visual impairment due to pathogenic variants of over 300 different genes. Accurately identifying the causative gene and associated variant is crucial for the definitive diagnosis and subsequent selection of precise treatments. Consequently, well-validated genetic tests are required in the clinical practice. Here, we report the analytical and clinical validation of a next-generation sequencing targeted gene panel, the PrismGuide IRD Panel System. This system enables comprehensive genome profiling of 82 genes related to inherited retinal dystrophies. The PrismGuide IRD Panel System demonstrated 100% (n = 43) concordance with Sanger sequencing in detecting single-nucleotide variants, small insertions, and small deletions in the target genes and also in assessing their zygosity. It also identified copy-number loss in four out of five cases. When assessing precision, we evaluated the reproducibility of variant detection with 2,160 variants in 144 replicates and found 100% agreement in terms of single-nucleotide variants (n = 1,584) and small insertions and deletions (n = 576). Furthermore, the PrismGuide IRD Panel System generated sufficient read depth for variant calls across the purine-rich and highly repetitive open-reading frame 15 region of RPGR and detected all five variants tested. These results show that the PrismGuide IRD Panel System can accurately and consistently detect single-nucleotide variants and small insertions and deletions. Thus, the PrismGuide IRD Panel System could serve as useful tool that is applicable in clinical practice for identifying the causative genes based on the detection and interpretation of variants in patients with inherited retinal dystrophies and can contribute to a precise molecular diagnosis and targeted treatments.
遗传性视网膜营养不良是一组临床复杂且异质性的疾病，其特征是由于300多个不同基因的致病变异导致视力障碍。准确识别致病基因和相关变异对于明确诊断及后续选择精确治疗至关重要。因此，临床实践中需要经过充分验证的基因检测。在此，我们报告了一种下一代测序靶向基因panel——PrismGuide IRD Panel System的分析和临床验证。该系统能够对82个与遗传性视网膜营养不良相关的基因进行全面的基因组分析。PrismGuide IRD Panel System在检测目标基因中的单核苷酸变异、小插入和小缺失以及评估其纯合性方面与桑格测序显示出100%（n = 43）的一致性。它还在五分之四的病例中识别出拷贝数缺失。在评估准确性时，我们用144次重复中的2160个变异评估了变异检测的可重复性，发现单核苷酸变异（n = 1584）和小插入及缺失（n = 576）方面的一致性为100%。此外，PrismGuide IRD Panel System在富含嘌呤且高度重复的RPGR开放阅读框15区域产生了足够的读深度以进行变异调用，并检测到了所有测试的五个变异。这些结果表明，PrismGuide IRD Panel System能够准确且一致地检测单核苷酸变异以及小插入和小缺失。因此，PrismGuide IRD Panel System可作为一种有用的工具，适用于临床实践，通过检测和解释遗传性视网膜营养不良患者的变异来识别致病基因，并有助于进行精确的分子诊断和靶向治疗。
